[gmx-users] error ffg53a
Justin A. Lemkul
jalemkul at vt.edu
Wed Aug 27 17:45:06 CEST 2008
shahrbanoo karbalaee wrote:
> Dear justin
> as you wrote, the first I make tfe.topology with this force field by
> command pdb2gmx and pdbfile from prodrg.and add to box with spc.now I
> have the file spc and tfe.by command grommp I minimized this file .I
> got a file emsolve.after this ,I work on this peptide .
> pdb2gmx -f name -ter -ignh
> editconf -d 0.7
> genbox -cp box.gro -cs emsolve.gro -p 1vm52.top -o solvated.gro
> grompp -f em.mdp -p 1vm52.top -c solvated.gro -o em.tpr
> I thought the program read from tfe.itp in /share/top file then I
> rename it and add the tfe.itp is made by drg.but it isnot right.and
> els I add gd_20 to tfe.itp because the program got error this
> line.and gd_29 in 1vm52.top .
Now I see. The tfe.itp in /share/top uses ffgmx atom types and parameters,
hence why you are seeing 'HO,' which corresponds to the hydrogen of a hydroxyl
group. In your topology, you call "tfe.itp," but the tfe.itp that you posted
contains only position restraint information.
What you will want to do is the following:
1. Use the parameters from tfe.top that you posted, removing the force field
call and [ system ] and [ molecules ] sections, as well as any other #include
statements for things like spc.itp or whatever else. Rename this file something
2. Use #include "my_tfe.itp" in your system topology that contains your protein.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users